The three dimensional numerical model of thermal discharge water in the Changjiang estuary was established to simulate the transport and diffusion of thermal discharge water from the Huaneng Shidongkou first power plant under second-phase rebuild project and the whole power plants in the estuary in summertime, and analyze their impacts on the sensitive targets. The thermal discharge water transports and diffusions downstream along the south coast of the South Branch affected by the runoff and mixing. In the case of only considered the project, there appeared area of temperature rise of greater than 2.0℃ near the drain outlet, while the impact is weak and the temperature rise is only 0.04℃ in the water intake. The area of whole tide-averaged surface temperature rise of 3.0, 2.0 and 1.0℃ is 0.12, 0.60 and 1.42 km2, respectively. The tidal and week averaged temperature rise envelope of 1℃ does not enter the water source protection area of Chenhang reservoir. In the case of considered the whole power plants in the estuary, the area of temperature rise of greater than 1.0℃ is wider, mainly distributes along the south coast of the South Branch in 50 km range from Taicang power plants to the downstream coast of Waigaoqiao power plants. The temperature rise is significant and appears wider area of greater than 4℃ near the Huaneng power plants and downstream water. The areas of whole tide-averaged temperature rise of 3.0, 2.0, 1.0℃ reach 2.34, 4.16, 13.52 km2, respectively. The temperature rise is higher and stratification near the coast, and decreases off the coast along the sections cross the water intake and drain outlet of the project. The isotherm of temperature rise of 1℃ invades the water source protection area of Chenhang reservoir. The area of temperature rise of 1℃ averaged during spring, middle, neap and week reaches 1.9, 1.82, 1.75 and 1.83 km2 in the secondary water source reserve of Chenhang reservoir. There is no impact of thermal discharge water from the whole power plants in the Chnagjiang Estuary on the water source protection area of Qingcaosha and Dongfeng xisha reservoir, Jiuduansha wetland nature reserve and Chongming Estern shoal birds nature reserve.